Consequences
by Wraithfodder
Summary: Missing scenes and tag for season 3 episode “Misbegotten”… Sheppard reflects over the entire mess and the consequences of their actions.


TITLE: **Consequences**  
AUTHOR: Wraithfodder  
RATING: T (language)  
CATEGORY: Gen, angst  
SPOILERS: Third season, spoilers for "Misbegotten"  
NOTES: Big thanks to KodiakBear for her betaing assistance.

_Copyright Disclaimer_: The _Stargate Atlantis _characters, as presented on the series, belong to MGM, Sci Fi, and other registered copyright holders. No copyright infringement is meant or intended by the writing and posting of this material. I'm just borrowing the characters and the universe for a piece of non-profit 'fan fiction' and will return in one piece (well, usually). However, all original characters and story material are copyright to author. Please do not repost this fiction, in whole or in part, anywhere, without expression written permission of the author.

**SUMMARY: Tag to "Misbegotten." Sheppard mulls over the entire fiasco of a mission.**.

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**Consequences**

"You don't name 'em, so that way when you lop off their heads, you don't get upset." Corporal Wilkins had matter-of-factly told that to John Sheppard many years, as his flight crew had sat around, nursing lukewarm sodas as they wound down after a tough day in combat. Many years ago, a lifetime away, a galaxy away, in a dusty tent in Afghanistan. Life on the farm: chickens, cows, pigs… all food waiting for the slaughter. You didn't make pets out of them because it's easier to slaughter and eat cow number three then kill ole' Bessie.

That still hadn't stopped John from naming the Wraith. It was a bad habit, but the 'hey you' stuff just didn't work. Throughout history, one side invariably assigned dehumanizing names to the opposing side - easier to kill the enemy if you thought of them as less than human. In this case, the Wraith were less than human. Even in their new human form, minds and bodies stripped of the desire to suck the life from their prey, they were still wraith deep down inside unless they got a daily injection. They looked human – you could see the whites of their eyes – what was that old adage? 'Don't shoot till you see the whites of their eyes?' Bet Lieutenant Morrison didn't see any eyes, white or otherwise, before one of those damned wraith turned him into a dried up husk.

Wraith. Human. Hybrid. It hadn't mattered. The plan had never been to thaw the Wraith survivors from the hive ship, at least not in the foreseeable future, but in order to make the Wraith hive ship a viable means of defense, he'd agreed to McKay's request to take them out of stasis. And agreed to Elizabeth's insistence that the 'humans' be relocated to a nearby unpopulated planet. Ronon's blunt suggestion to deep-six the unconscious wraith survivors into the cold hard vacuum of space hadn't been met well by anyone, at least not out loud, although Sheppard could understand where that mentality came from: years on the run, the Satedan living his entire life fighting against beings that lived to decimate the human race. Plus seeing friends die in front of you. The thought of two hundred less Wraith in the universe didn't bother Sheppard at all, because unless Beckett could find a one-shot deal to make the wraith permanently human, the survivors would eventually regress right back to their nice little soul-sucking selves.

At least isolated on a planet, they could do no real harm. John had thought that, had told Beckett point blank that only so much time and resources would be devoted to those 'survivors.' And how many times had he told 'Lathon' – one of the Wraith survivors – the same old tired lie about plagues and potential cures and why they had to stay isolated? Far too many times to count, or at least it seemed that way. Every time John visited the camp he couldn't help but feel like he was a wary mouse creeping past a pack of hungry foxes. While the injections kept the wraith blissfully unaware of their previous lifestyle, it also kept them docile and at times, confused. They couldn't suck the life out of a man but there were more than enough of them to overpower anybody by sheer number alone. It was that thought that kept him on edge, his finger on the P90's trigger, the safety off. Made him nearly jump out of skin and bring up his weapon when Lathon innocently tapped him on the shoulder.

Damn. He should have never acquiesced to Carson's insistence that the doctor work on a solution for the problem. Should have just dumped the survivors on that planet, let them fend for themselves, but then found out that if enough Wraith got together for a party, they could send for take-out without a phone. Live and learn, he'd replied sourly to Teyla, but in this galaxy, you rarely got the chance to do the latter.

But leave it to a bunch of bureaucratic second-guessing ass-kissers back on earth to dump one of their weasel spies on Atlantis to 'talk' to Elizabeth's staff. To interrogate him and his team about Elizabeth's actions and suggest - without the benefit of having actually had a wraith hand wrapped around their throat, or watch a man die hideously in front of their eyes – and have the gall to call their recent actions a 'science project' and then second guess their life or death decisions? John had kept his answers very terse after that while he'd fought down the escalating desire to take Woolsey's pen and snap it in two, and then punch the man in the face.

The whole damn situation was so FUBARed that he really shouldn't have been surprised that a Wraith ship would show on the long range sensors in their back yard, that they'd race back to that planet to discover that the inmates had taken over the asylum, sucked the very life from their men and taken Beckett hostage.

He'd had no compunction whatsoever of ordering a nuke loaded onto the jumper before they'd launched the rescue mission. Us or them. It was a nasty mentality, but it was the only one that would leave them alive. Rescue their people and eliminate the Wraith. Neither Ronon nor Teyla had batted an eye, although Teyla's eyes did darken at his order of what might technically be a mass murder. McKay had simply averted his gaze, but he could tell the scientist was bothered to a degree, yet then he got busy with trying to get the damn hive ship to obey his command. If they didn't get there before the other wraith ship, they were all going to be screwed. Big time major screwed, and bureaucratic lackies putzing about Atlantis making ill-informed judgments would be the least of their worries.

Total annihilation. That's what the nuke would have guaranteed them had the device gone off, but apparently Michael had learned too well from his time on Atlantis. Damned if John could figure out where the wraith had found schematics for earth-based weapons. Oh wait, yeah, the Wraith ship had uploaded files from Atlantis during that disastrous 'alliance.'

Fuck.

John maneuvered the jumper again, dodging another chunk of hive ship before it could pulverize their ship and them with it. They'd been out there in space for half an hour now, biding their time. The hive ship had hung around for a while, sending their darts down to where they'd been aiming their salvo of energy pulses. God, he hoped they'd found no survivors, wouldn't find out that Atlantis still existed. They were plumb out of any rabbits to yank out of the proverbial hat to save themselves again.

Michael had helped him rescue Rodney and Ronon on the hive ship, but the act had been one as much from self-preservation as anything else. Had the wraith really expected to have free run of Atlantis upon returning? That they would let him go with everything he knew? Teyla had told John about Michael's demand for a ship so that he could flee the city. Ronon had volunteered to put the wraith out of his misery upon hearing that, but Michael was the only wraith they had history with who _might_ come in handy later on. Just drug him up, turn him human and then… John hadn't known what 'then.' Neither had Elizabeth.

Another chunk of crispy hive ship floated past, its blackened underside nearly blending into the vastness of the universe. Damn, who would have guessed you could turn something the side of Rhode Island into so many little pieces? Well, maybe not the size of Rhode Island maybe, but damned big. Footfall field size if nothing else. What bugged him was that the Wraith hadn't even bothered to give their ship a call before blasting them, but then again, maybe whatever message Michael's little group had sent had included 'Bad people in hive ship. Please kill. Thank you very much. Michael."

What had happened down on that planet? And when had it all gone to hell? The wraith reverting – he could figure that out. Everything with wraith ended badly and maybe he should give Ronon standing orders to beat him black and blue if he ever said the words 'alliance with wraith' ever again. And stun him too.

But Carson….the poor man had been sporting darkening bruises around his wrists and ankles from where he'd been strapped down to the gurney, and those bruises weren't just a couple hours old. Ronon had slung the unconscious doctor over his shoulder as they ran back toward the cloaked jumper, all of them alarmed for those several minutes that they'd run into a massive group of wraith and it would all be over. It was only when they broke into space that Carson began to pull himself to consciousness. Teyla had administered oxygen, but that wasn't the problem. The man had been traumatized, not physically, but…not a scratch on him, strapped down to a gurney? Two plus two equals bad news. Sheppard had unfortunately had a taste of a Wraith mind probe before…. invasive, terrifying, even painful to a degree, but each time he'd been lucky enough not to have had the full treatment, but Carson….

The physician had woken up and gotten his wits back by the time they arrived at the hive ship, though he was strangely quiet. He just nodded his head when Teyla inquired if he was okay. Okay? Okay? Yeah, Carson was as 'okay' as a potato salad left out in the full sun for two days straight.

And then Carson had actually wanted them to jeopardize their lives to go back and save the wraith that were still human? Over a hundred men believed that "we are their saviors," he'd insisted. _Saviors!_ John had wanted to shout back in anger: "And what about _our_ men, Carson? Actual _human _beings who got the fucking life sucked out of them protecting you? Did you know that Lieutenant Morrison had a five-year old niece who loves smurfs and kittens? Yeah, learned that on his one-way trip over to the planet when he was showing his men some pictures of her." But he'd kept his mouth shut, masked any emotion he felt choking at him and thanked God that Ronon backed him up. "Casualties of war," the Satedan had bluntly explained. Damned if he was going to let anyone from Atlantis become another casualty to save a wraith, reverted or not. But it still felt like a knife twisted painfully into his gut as he caught the look of abject misery that crossed Carson's face when he told Rodney to press the button.

Despite everything those damned wraith had done to him, Carson still somehow held on to his hope and humanity, even toward the enemy; John only wished he could say the same about himself. It felt like the whole catastrophe had seared another layer off his soul, something he could never get back, making him wonder if one day he might end up like Ronon, consumed by an undying hatred for the enemy.

The trip back to Atlantis was going to take…. He didn't even want to do the math. McKay's crestfallen face didn't bode well as he'd obviously done the math too. How could a genius not extrapolate the facts? They'd be starving by the time they got back, but they'd be alive. When the wraith salvo had punctured the hull of their hive ship and air began to vent, there wasn't much choice but to jump ship in the cloaked jumper, then get a more than respectable distance away and watch another highly technological ship get blown to smithereens. First the Orion, then the hive ship. Thank god they didn't have to pay insurance or else they'd be in the high, _high_ risk pool. Finally, the remaining hive ship left and he dove the jumper smoothly into the murky atmosphere, down toward the base camp. Rodney had been correct; he _could_ get a better lock on the planet than a floating object in space.

The atmosphere in the jumper's suddenly claustrophobic cabin had gone to dead silence, save for a short gasp from Carson, as they surveyed the damage wrought by their attack. Deep craters the size of mall parking lots dotted the landscape. Trees were splintered and cast about like toothpicks. Brown soil has been turned to black soot. John kept the jumper high enough to use its instruments to survey for human or wraith life. None appeared, and it wasn't necessary to see possible dismembered bodies to confirm death. Sensors indicated that nobody had survived - or had the darts done some house cleaning? He knew everybody was thinking the same dismal thought as they back toward space, and the long, arduous trek toward home.

Carson had begun pacing like a caged animal around the back of the jumper after that. He couldn't sit down. Everybody offered him a seat, even Rodney, which was rather surprising as it was difficult to pry the scientist from any seat, but Beckett just said evenly "I've done enough lying around, thank you," leaving them in a pall of uncomfortable silence. Restraints, dark bruises. Bad, bad times.

The pacing continued and John was sorely tempted to tell him to 'Please sit. You're driving me nuts, and it's a long trip home,' but if it let the doctor work out his frustration, or wore him into utter exhaustion until he couldn't stay awake any longer, Sheppard was all for it. In looking around, he saw that Rodney's pained expression seemed to agree with his dismal thoughts, while Teyla seemed hard pressed not to physically grab Beckett and plunk him down in a seat to tell him it would all be okay. She was damned good at that, and at times, even if the world was two seconds shy of being blown up, you might even believe her. He'd been there himself.

John took one last look through the window at the massive chunks of dead hive ship. It was going to be a really long journey through empty space. They needed to—

A massive flux of green and white light flared in the black distance. Telltale tendrils of jagged white tore from its edges: a hyperspace window. Shit! Couldn't the wraith give them any peace?

"Oh thank God," exclaimed Rodney.

The incredibly welcome visage of the Daedalus emerged from the spatial window. It looked like a toy compared to the once massive hive ship, but what was foremost in John's mind was that they were being rescued and he drank up the ship's rapid movement toward their position like a dehydrated man desperately sucking downing a glass of ice cold water.

"Are we going to gawk at it _all_ day?"

Rodney's irate voice echoed behind him, while Teyla's slight cough hinted that he really should do something practical, so he rotated the jumper into docking position and called the Daedalus. Caldwell seemed pleased to know that John's team hadn't been obliterated. They exchanged the usual banal pleasantries – simple stuff like 'where the hell are you?' and then the embarrassment of realizing he still had the jumper cloaked, to a lame comment about 'long rides home.' Now wasn't the time to say, 'Gee, Colonel Caldwell, the whole trip sucked big time. Lost another spaceship, but who really cares because we lost several good men, got another good man who went through who knows what kind of hell, and is there any hard liquor on board the Daedalus as for once I'd really like to get drunk out of my mind to forget it all?'

Everybody looked thrilled about the rescue, except for Carson. That same intense, grim expression hadn't left his face since surveying the destroyed camp.

John wasted no time in slotting the tiny jumper into the Daedalus' bay next to some F302s.

Not amazingly, Rodney was the first to debark, going on about food and starvation and blood sugar levels plummeting to the depth of the Mariana trench. As his feet hit the solid floor of the bay, the scientist turned. "Come on, Carson, before the grunts eat up all the good food."

Teyla stood and moved toward the physician. John gently snagged her by the arm. "Stay with him," he said quietly to her.

The Athosian frowned slightly, but smiled, resting a hand briefly on his upper arm. "You know you do not need to ask." She went over to Carson, carefully wrapping her arm around his elbow. He offered no resistance as the pair left the jumper.

Ronon directed a 'are you coming?' type glare at him and John followed, a part of his mind set at ease by the familiar surroundings: Earth-based technologies, bright lights, and _no _cocoons. He could live the rest of his life and then some without ever seeing a cocoon again. He didn't know how long the memory of seeing those torn-open cocoons aboard the hive ship would stay with him. Thank God that Ronon knew how to hide knives on his person.

Both Teyla and Beckett left through the bay door into the corridor beyond, while Rodney slowed down, hanging back until both Ronon and John caught up with him and they stopped.

"Thought you were hungry?" Ronon directed amusingly at McKay.

"Am. Was." Rodney took a PowerBar out of his vest pocket, ripped open the foil wrapping and bit off a large piece. "This'll do," he mumbled through the chewy substance. He cast a worried glance down the long narrow corridor.

John's feet felt glued to the floor, but he forced himself to continue walking. The others followed, taking his lead. He wasn't sure if they should go to the infirmary, which is where he knew Teyla was taking Beckett. Part of him knew that his presence would be the least comforting one for Carson. He'd argued with Carson over the viability of the whole experiment, had cut him out of the decision in which he took responsibility for taking the lives of over one hundred … people. Had Woolsey been right? Even he couldn't accept the human-wraith as completely human, but it wasn't as though he hadn't taken human lives before. When he'd shut the gate's iris, condemning over 50 Genii to death.

Yet when confronted with a human Michael again… he'd had to dampen down feelings of hatred and confusion when Michael – in his amnesiac and harmless form – politely asked questions at the camp. Even on the hive ship, when Michael had been a pure Wraith, it had been hard _not_ to remember that singular moment when Michael had nearly killed Teyla. He'd let Michael help him aboard the ship, used him as a tool. Did what he had to in order to survive.

"Do you… did they…?" Rodney stammered..

"Don't know," Ronon replied bluntly.

No. None of them knew what happened at the camp while Carson had been the only real human left, or why an indefinable haunted expression seemed to permeate the man's very being. Maybe Teyla could get it out of him, maybe not, but it would have to happen. They would need to know in the end, but it would be his team – _his_ people – who would encourage the man to talk, and if Carson wanted to scream at them, tell John he was a bloody murderer for consigning over a hundred men to death, then so be it. Carson wasn't a soldier and god forbid if that day ever came.

Neither was Rodney. The scientist quickly ate the rest of his PowerBar and began to pat down his vest for more food. John reached into one of his vest pockets and handed over a bar, which Rodney snatched and dug into as though his life depended upon its consumption. Nervous eating. John was hungry too. Couldn't remember when he'd last had a decent sleep, last time he'd had more than one bite of one of those gluey bars, or hadn't felt trapped on a razor's edge from the ever-increasing escalation of the disaster that was unfolding.

Rodney hadn't been keen on nuking the camp, at least not with people still in it, but he'd complied with John's order without any real hesitation. He'd seen up close the horrors of what the Wraith could do to a human being, had been trapped in one of those blasted cocoons awaiting a fast but hideous death, but only after the ship reached Earth and he'd been forced to watch his planet's destruction. Rodney had told John about that wraith's horrible promise after they'd gotten back to Atlantis and instead of sleeping, Rodney had spent the evening overdosing on coffee so he wouldn't sleep and have nightmares. But even coffee couldn't keep you awake forever, and in his foggy about-to-pass-out mode, rambled on about how he would have been solely responsible for the utter annihilation of every last ounce of coffee in the world. John had known precisely what he'd meant, but sometimes Rodney made strange analogies when his brain wasn't functioning properly.

Ronon said that Rodney had been really helpful in their escape; he'd whined so much that Ronon had had an overwhelming desire to break free and throttle the scientist just to shut him up. Ronon was dealing with the entire fiasco better than anyone else, but then again what could be worse than being hunted down by the wraith for seven years? To never know peace?

They were fifteen feet from the infirmary's front entrance when Caldwell's voice sounded loud in his earpiece.

"Yes, Colonel?" said Sheppard, stopping in his tracks. One part of him was thankful for the reprieve but another part was ticked off as he knew should have checked in immediately.

"Colonel. The debriefing," came Caldwell's simple but authoritative prod.

"Taking a detour to the infirmary, so it's just going to have to wait," shot back John. Shit. He winced in frustration and simmering anger. That wasn't Elizabeth he was talking back to. She'd understand his decision but Caldwell would--.

"Understood," came back the reply

"Uh, thank you, sir," Sheppard stumbled after a second.

"When you're ready," signed off Caldwell.

Both Ronon and Rodney were staring at him in undisguised curiosity. "What?" Rodney mumbled through another bite.

"Nothing." Debriefings, breakdowns, a dissection of a botched mission that the Woolsey character would no doubt lap up in delight. What had John called his attack on the wraith hive ship? Mission 'things are going to screw up'? He couldn't even remember but it was so appropriate now it was painful.

John proceeded to the doorway but paused, looking in, frowning at what he saw. Across the sterile, well-lit infirmary, Carson was lying on one of the beds with several medical personnel swarming around him. He wasn't escaping but then he wasn't really making an effort either. And throughout the quiet but calm murmurings he heard from the medical staff, Teyla stood beside him, a steady grasp on his hand that the medical personnel seemed to understand.

An anchor in the storm.

John silently pulled back out into the corridor, earning him a confused and questioning glare from Rodney. "I think the idea is to go inside?"

"You go," said John.

Rodney glared at John, then at the tall Satedan, who seemed to be of no help, but John realized that Ronon didn't need an explanation. He understood well enough why Sheppard had retreated.

"I'm the last person Carson needs to see right now, Rodney," said John quietly, his mind replaying the terse almost one-sided arguments down on the planet. That John would have no problem abandoning the 'people' on that world and let them revert back to their wraith origin, and the lethal consequences of that decision. "He spent the last several days working to save people who I just blew up."

"Oh," said Rodney simply. But it wasn't an 'oh, that is so insane, of course Beckett wants to see us all and he'll understand why we did what we did' but an 'oh,' quiet and full of unspoken meaning, as Rodney's mind no doubt processed the events of the last few days and the terrible cost it had exacted from Carson, and quite honestly, the rest of them. The scientist stuffed the PowerBar wrapper in his hand into his vest. Its foil crinkled noisily in the sterile air.

"So?" Ronon spoke up, his gruff voice breaking the tense silence.

John found himself staring aimlessly at the gray wall behind Rodney. Now what? Hope to God that the wraith all died on the planet's surface, that not a one remained to spill the beans on Atlantis, or worse, Earth's position? That if the wraith did find any humans down there, that they were instantly turned into meals? Who would have thought he'd be rooting for the wraith to do that?

Rodney coughed, drawing John from his dark thoughts. "Go ahead, Rodney." Not that the man needed permission, but perhaps reassurance. Carson wouldn't blame him for what had been Sheppard's decision, and John knew that despite all he'd been through as well, Rodney would need someone to assure him as well.

Only John wasn't the one to do it, not right now.

As Rodney disappeared into the infirmary, John turned on his heel, aware that Ronon was following.

"Hungry," the Satedan said drolly. He handled this crap much better than the rest of them. Kill all wraith. Simple as that. "You?"

"I'm going to… unwind."

Ronon just grunted in acknowledgement, then peeled off at the second corridor toward the small mess hall on board the ship.

It wouldn't be long before Caldwell would realize that John was AWOL from the infirmary, but it would give him enough time to beat the crap out of the only punching bag located in the small gym someone had thankfully designed into the Daedalus' blueprints. You couldn't stay on a ship this size for weeks on end without some way of relieving the stress.

It didn't take long to get to the ship's gym, tucked away in a less traveled area, which suited John just fine. It was empty, which was even better. John shucked his weapons and jacket, tossing them into a corner as he set his sights on the lone punching bag secured in one corner of the room.

They'd survived by the skin of their teeth – but the vision of several dogtags dangling ominously from Ronon's hands drove home the true loss of what trying to save those hundred or so 'humans' had cost.

John slammed a fist into the solid bag, ignoring the sharp sting that dragged across his knuckles. His mind felt mired in darkness as the repercussions of the decisions made – many of them his own – stabbed away at his thoughts. Had all the wraith died on that planet? It was impossible to know.

He slammed into the bag again, realizing that the razor's edge of fine fear would once again cast its pall over Atlantis, with the knowledge that one of the wraith could have escaped, that another siege might occur.

He punched the bag again and again… his anger mounting… for Morrison, for the young girl who would never see her uncle again, for all the fuckups that had lead to this point, but mostly, for what the wraith might have taken away from Carson.. and the sad fact, as he began to pummel the bag, he wasn't sure what that was.

THE END

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